Need help with gas particle simulation
Final result



Sorry for the gif quality.

Overview

You can use Rigid Bodies simulation to achieve something similar. I'll write an overview of methods I've used. Ask if you need more steps. 

Each bold text could be treated as a keyword for searching in Blender Manual.

I will use metric system for measurements.

You result may vary. Slight differences in models could bring some problems (or not) as "physics" in Blender isn't real physics.


  Remember to Apply Scale for every object.


World

Turn off Gravity (or set it to 0). 

Speed will control... Speed of animation.

Steps per second and Solver iterations will increase quality.



A box

Model:

Simple Cube 2x2m with Inverted Normals. I've assigned two materials to it. One for base color and one for front face (Transparent Shader).

Rigid Body:

Set Type to Passive and Shape to Mesh. Change margin to something around 5cm, this should help with keeping molecules inside the box. Friction to 0. We don't want any.



Molecules

Model:

Again, nothing fancy. Three Spheres joined together with assigned two materials. Size around 13x8x8cm. Duplicated couple of times. Duplicate it after setting Rigid Body values.

Rigid Body:

Similar to the box but. Type is Active, Margin 1mm or none, Mass 1g.

"Activator"

I've used Force Field > Force with keyframed Strength. At frame 1 Strength is -0.3 and at frame 10 it's 0. 

Such setting allows us to pull molecules to the center of the box and after 10 frame Force Field is deactivated and molecules are living on their own. You can also try positive value to push molecules but this could bring some problems and molecules will be pushed outside the box.